rs2733834

chr9-12708910-C-Gchr9-12708910-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000550.3(TYRP1):c.1409-67C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 1,368,220 control chromosomes in the GnomAD database, including 260,194 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.49 (21835 hom., cov: 34)
  • Exomes 𝑓: 0.60 (238359 hom.)
• Consequence: TYRP1 NM_000550.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.34

Genes affected

TYRP1 (HGNC:12450): (tyrosinase related protein 1) This gene encodes a melanosomal enzyme that belongs to the tyrosinase family and plays an important role in the melanin biosynthetic pathway. Defects in this gene are the cause of rufous oculocutaneous albinism and oculocutaneous albinism type III. [provided by RefSeq, Mar 2009]

LURAP1L-AS1 (HGNC:49761): (LURAP1L antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.671 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TYRP1	NM_000550.3	c.1409-67C>G		intron_variant		ENST00000388918.10
LURAP1L-AS1	NR_125775.1	n.317-8284G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TYRP1	ENST00000388918.10	c.1409-67C>G		intron_variant		1	NM_000550.3	P1
LURAP1L-AS1	ENST00000417638.1	n.273-8284G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73877 AN: 151810 Hom.: 21826 Cov.: 34

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.487

GnomAD4 exome AF: 0.602 AC: 732752 AN: 1216292 Hom.: 238359 AF XY: 0.593 AC XY: 363013 AN XY: 612430

Gnomad4 AFR exome AF: 0.207

Gnomad4 AMR exome AF: 0.440

Gnomad4 ASJ exome AF: 0.565

Gnomad4 EAS exome AF: 0.00427

Gnomad4 SAS exome AF: 0.268

Gnomad4 FIN exome AF: 0.714

Gnomad4 NFE exome AF: 0.673

Gnomad4 OTH exome AF: 0.550

GnomAD4 genome AF: 0.487 AC: 73914 AN: 151928 Hom.: 21835 Cov.: 34 AF XY: 0.479 AC XY: 35577 AN XY: 74252

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.676

Gnomad4 OTH AF: 0.482

Alfa AF: 0.490 Hom.: 1826

Bravo AF: 0.458

Asia WGS AF: 0.143 AC: 500 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
Cadd	Benign	0.049
Dann	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2733834; hg19: chr9-12708910;